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rate=15794117.65/min [8960000], rate=15811764.71/min [8970000], rate=15829411.76/min [8980000], rate=15847058.82/min [8990000], rate=15864705.88/min [9000000], rate=15882352.94/min [9010000], rate=15900000.00/min [9020000], rate=15462857.14/min [9030000], rate=15480000.00/min [9040000], rate=15497142.86/min [9050000], rate=15514285.71/min [9060000], rate=15531428.57/min [9070000], rate=15548571.43/min [9080000], rate=15565714.29/min [9090000], rate=15582857.14/min [9100000], rate=15600000.00/min [9110000], rate=15617142.86/min [9120000], rate=15634285.71/min [9130000], rate=15651428.57/min [9140000], rate=15668571.43/min [9150000], rate=15685714.29/min [9160000], rate=15702857.14/min [9170000], rate=15720000.00/min [9180000], rate=15737142.86/min [9190000], rate=15754285.71/min [9200000], rate=15771428.57/min [9210000], rate=15788571.43/min [9220000], rate=15805714.29/min [9230000], rate=15822857.14/min [9240000], rate=15840000.00/min [9250000], rate=15857142.86/min [9260000], rate=15874285.71/min [9270000], rate=15891428.57/min [9280000], rate=15908571.43/min [9290000], rate=15483333.33/min [9300000], rate=15500000.00/min [9310000], rate=15516666.67/min [9320000], rate=15533333.33/min [9330000], rate=15550000.00/min [9340000], rate=15566666.67/min [9350000], rate=15583333.33/min [9360000], rate=15600000.00/min [9370000], rate=15616666.67/min [9380000], rate=15633333.33/min [9390000], rate=15650000.00/min [9400000], rate=15666666.67/min [9410000], rate=15683333.33/min [9420000], rate=15700000.00/min [9430000], rate=15716666.67/min [9440000], rate=15733333.33/min [9450000], rate=15750000.00/min [9460000], rate=15766666.67/min [9470000], rate=15783333.33/min [9480000], rate=15800000.00/min [9490000], rate=15816666.67/min [9500000], rate=15833333.33/min [9510000], rate=15850000.00/min [9520000], rate=15866666.67/min [9530000], rate=15883333.33/min [9540000], rate=15900000.00/min [9550000], rate=15916666.67/min [9560000], rate=15933333.33/min [9570000], rate=15950000.00/min [9580000], rate=15966666.67/min [9590000], rate=15983333.33/min [9600000], rate=16000000.00/min [9610000], rate=15583783.78/min [9620000], rate=15600000.00/min [9630000], rate=15616216.22/min [9640000], rate=15632432.43/min [9650000], rate=15648648.65/min [9660000], rate=15664864.86/min [9670000], rate=15681081.08/min [9680000], rate=15697297.30/min [9690000], rate=15713513.51/min [9700000], rate=15729729.73/min [9710000], rate=15745945.95/min [9720000], rate=15762162.16/min [9730000], rate=15778378.38/min [9740000], rate=15794594.59/min [9750000], rate=15810810.81/min [9760000], rate=15827027.03/min [9770000], rate=15843243.24/min [9780000], rate=15859459.46/min 08:55:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns: identified 7756 cancer introns 08:55:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:55:37 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:55:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:55:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:55:37 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:55:37 : INFO : -found 2567 cancer introns 08:55:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:55:38 : INFO : Creating the BED File. 08:55:43 : INFO : Saving Bed File as 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:55:44 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:55:44 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:55:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:15:20 : INFO : Execution Time = 19.61 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bNS-T1-TRNA-1_B23MHV2LT4_1 09:15:20 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:15:20 : INFO : Running: samtools sort -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:15:21 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:15:21 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:15:21 : INFO : Running: samtools sort -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam [bam_sort_core] merging from 107 files and 1 in-memory blocks... 09:38:31 : INFO : Execution Time = 23.18 minutes. CMD: samtools sort -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam 09:38:31 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_gene_reads.ok 09:38:31 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam Done with chr chr1. Done with chr chr2. Done with chr chr3. Done with chr chr4. Done with chr chr5. Done with chr chr6. Done with chr chr7. Done with chr chr8. Done with chr chr9. Done with chr chr10. Done with chr chr11. Done with chr chr12. Done with chr chr13. Done with chr chr14. Done with chr chr15. Done with chr chr16. Done with chr chr17. Done with chr chr18. Done with chr chr19. Done with chr chr20. Done with chr chr21. Done with chr chr22. 09:45:20 : INFO : Execution Time = 6.82 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 09:45:20 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp.ok 09:45:20 : INFO : Running: samtools sort -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp [bam_sort_core] merging from 3 files and 1 in-memory blocks... 09:46:05 : INFO : Execution Time = 0.75 minutes. CMD: samtools sort -o 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmp 09:46:05 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok 09:46:05 : INFO : Running: samtools index 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 09:46:10 : INFO : Execution Time = 0.08 minutes. CMD: samtools index 659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam 09:46:10 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bNS-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.sifted.bam.indexed.ok 09:46:10 : INFO : Running: samtools index 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 09:46:10 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 09:46:10 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/659_bNS-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam.indexed.ok 09:46:10 : INFO : Running: create_report 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bNS-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bNS-T1-TRNA-1_B23MHV2LT4_1' 09:51:48 : INFO : Execution Time = 5.63 minutes. CMD: create_report 659_bNS-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bNS-T1-TRNA-1_B23MHV2LT4_1.ctat-splicing.igv.html --track-config 659_bNS-T1-TRNA-1_B23MHV2LT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bNS-T1-TRNA-1_B23MHV2LT4_1' 09:51:48 : INFO : Running: touch /tmp/nxf.7F6jAy4feB/659_bNS-T1-TRNA-1_B23MHV2LT4_1.chckpts/igv_create_html.ok 09:51:48 : INFO : done.